I've been thinking about the Stirling within this thread; it certainly has merit. Four engines, heavy bomb load, good range, comparable speed to other bombers of the time, power operated turrets, easy to fly, manoeuvrable with a good roll rate for such a big aeroplane; pilots commented favourably about it and compared it to a Gentleman's Carriage, so with all these things, is worthy of inclusion. Its down side is its poor ceiling, which made it flak bait, but it held the line, along with the Halifax until more suitable and less vulnerable and troublesome Lancasters were available in numbers from 1942 on. The addition of armour plating and other equipment introduced during service reduced its rate of climb and ceiling further, but it remained well liked by aircrew, despite a lack of enthusiasm from the Air Ministry. Although not really a criteria for judgment here, the Stirling took a long time to get right for production (there were also delays as materials were diverted from manufacture of fighters around the Battle of Britain time by the Ministry of Aircraft Production) and for some reason it cost more to build than either the Hali or Lanc. Despite this, by the end of 1941, some 150 Stirlings had been manufactured, which gave better availability than the Halifax by a country mile. It was not plagued by any catastrophic mechanical defect, like the Manchester or Halifax either.
Regarding the Fortress, the RAF's experience with the Fort I was disappointing, but one of the principal criticisms by the Americans was the fact that it was sent on individual sorties. It's equipment froze at high altitudes and was criticised for its defensive armament - a big minus. It's worth remembering that the RAF used it on daylight raids individually, which was asking for trouble; it received 20 of 38 B-17Cs built by that time, so wasn't available in large numbers. The Americans also claimed the RAF was using it above its designed operating height and that defensively, the tactics employed could not take advantage of its defensive armament as well as the Americans had planned.
On the plus side, it had an excellent turn of speed for a big bomber, a maximum of 320 mph at 20,000 feet and cruise of 232 mph at 14,000 feet; putting that into context, this was 1 or 2 mph difference from the maximum speed of the Wellington. Despite its comparatively small bomb load, it did have impressive range of 2,100 mph and a maximum range of 3,160 miles. If it were put to use in a different fashion, it could, or would have been very effective if these attributes were exploited.
Agree, Glider about the Boston, a very practicable and adaptable aeroplane, but is slightly outside the scope of this thread as a bomber at least. By mid 1940 the French had received some 64 (65 in some sources) DB-7s before the country had capitulate; these did carry out combat ops against the advancing Germans though, the ones that arrived in Britain from the French order had to have their throttle movement reversed, the French moved the power levers aft for increased, so this delayed entry into service. The RAF used these 20 examples for training only as Boston Is as they were considered unfit for service. The RAF Boston II was similar to the earlier Boston I but had uprated engines and was used exclusively as a heavy fighter and was named Havoc I as a night fighter in RAF service. The first bomber version in RAF service was the Boston III - the USAAC received the A-20C, which was close to the Boston III in performance and spec - and although the first Boston IIIs/A-20Cs were delivered in 1941, they weren't quite ready for operations until early 1942.
The TB-3 is not worth mentioning; it was considered obsolete in 1939. The TB-7 or Petlyakov Pe-8 is an interesting choice, but is in service in paltry numbers in 1941 - only a small number were available due to engine and production issues. At the time of Barbarossa, only the 2nd Sqn of the 14th heavy Regiment had them in service, but none were ready for combat. Later in the year, as aircraft became available - fourteen in October 1941, night raids were conducted, even against Berlin, but results were unspectacular. It had good bomb load, range and performance and showed much promise though, but I would be reluctant to include it as one of the three best of the year, largely because of low numbers and poor operational availability.
A further rethink from me. Wellington, Stirling and a toss up between Fortress I and B-24C... Hmmm, thing is, neither Fort or B-24 available in numbers and poor defensive armament. Maybe Wellington, Whitley, Stirling? An all-British top three? All available in numbers, relatively trouble free service use in 1941, defensive turrets, good bomb load, good range...